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Important! Template update for nf-core/tools v3.4.0#879

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nf-core-template-merge-3.4.0
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Important! Template update for nf-core/tools v3.4.0#879
nf-core-bot wants to merge 3 commits into
devfrom
nf-core-template-merge-3.4.0

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@nf-core-bot

@nf-core-bot nf-core-bot commented Oct 15, 2025

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Version 3.4.0 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.4.0 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.4.0 release page.

@jfy133

jfy133 commented Oct 16, 2025

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@nf-core-bot fix linting

@github-actions

github-actions Bot commented Oct 16, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 4be4c37

+| ✅ 371 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • rocrate_readme_sync - The RO-Crate descriptions do not match the README.md content. Use nf-core pipelines lint --fix rocrate_readme_sync to update.

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.0
  • Run at 2025-10-16 08:29:48

@nf-core-bot

nf-core-bot commented Oct 16, 2025

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Version 3.4.1 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of #880

Please use #880 to merge in the new changes from the nf-core template as soon as possible.

@dialvarezs dialvarezs deleted the nf-core-template-merge-3.4.0 branch November 21, 2025 11:36
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@jfy133 jfy133 Awaiting requested review from jfy133 jfy133 is a code owner

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